Description

Constructs a graph from a reference and variant calls or a multiple sequence alignment file

Input

name:type
description
pattern

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

input{:bash}

:list

Either one or more VCF files containing different contigs or a multiple sequence alignment file

*.{vcf.gz,fa,fasta,fna,clustal}

tbis{:bash}

:list

The index files for the VCF files

*.tbi

insertions_fasta{:bash}

:file

A FASTA file containing insertion sequences (referred to in the VCF file(s))

*.{fa,fasta,fna}

meta2{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

fasta{:bash}

:file

The reference FASTA file (cannot be used in combination with msa, but is required when using vcfs)

*.{fa,fasta,fna}

meta3{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

fasta_fai{:bash}

:file

The index of the reference FASTA file

*.fai

Output

name:type
description
pattern

graph{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.vg{:bash}

:file

The constructed graph

*.vg

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

vg
MIT

Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods.

github.com/vgteam/vg github.com/vgteam/vg/wiki
maintainer
Github user nvnieuwk
get in touch
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